Stowers trailed leader Hubbard by 7kg after the snatch, but she went onto claim gold after her New Zealand rival pulled out of the competition with an injured left elbow.
New Zealand's Hubbard, the first transgender athlete to compete at the Commonwealth Games, was expected to win the event easily.
She withdrew after hurting her arm on her final snatch, which saw her miss her attempt at a Commonwealth record of 132kg and twist her elbow as she dropped the bar behind her.
Hubbard left the platform in pain and received treatment in the 10-minute break prior to the clean and jerk round.
Stowers, 17, went onto manage 140kg in the clean and jerk, giving her a total of 253kg.
"I never thought I could compete against Laurel because of her high total," she said.
"After the snatch when she pulled out, all I did was focus on each lift and try to do the best I could on the platform.
"I was very shocked when she withdrew after the snatch.
"It meant I was in the lead and I knew I had a good chance of the gold medal."
Samoan team official Mary Opeloge said it was unfair for Hubbard to compete.
"I hope everyone noticed [that it was unfair]," she said.
"But all Feagaiga wanted to do was her best."
Nauru’s Charisma Amoe-Tarrant finished second with a total of 243kg, securing her country’s first medal of Gold Coast 2018
Her final clean and jerk lift at 142kg took her above England’s Emily Campbell, who finished third with 242kg.
Hubbard was eligible to compete at Gold Coast 2018 because she passed the International Olympic Committee criteria for transgender athletes after proving her testosterone levels stayed below certain levels in the 12 months leading up to the event.
Despite her disappointment, she said she has no regrets.
"It's obviously a difficult time," the 40-year-old added.
"But the one thing I am happiest about is that I tried to reach for my best performance.
"This happens sometimes, but that's the sport.
"We can always go back over these things in our heads, but the truth is that unless we try to be the best person we can be, the best athlete, then really we are not being true to sport.
"I am happy with the decisions I made today.
"I have no regrets.
"Medals are only one measure of performance.
"I am obviously unhappy I had to withdraw, but I gave it everything I had and I can sleep well knowing that."
Stowers’ victory secured Samoa's second gold medal of the Games.